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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattatatagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA

Basic information

species Glycine max
transcript GLYMA01G29470.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 3
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattatatagtgttagcaattgatggtagttcttataaatgtctt-gcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
 |||    | | | | |      ||   ||| ||   || ||     |    || ||   | |||       |||  | ||| || || ||  ||| |||| | ||||| || || ||||||||||| |||||||| ||||| ||||||||||| |   | || ||||| |||||| |||| || |||||||||||  |  
tattcaaagtggtatacacctcgttatgttactgatatatttatgatatttgat-attcggagttgcattcagataattgtttttctacattcctttgcagATCCCACGCTTATATAATGTGTACAAGGAAATGGGTATTGTTACATCATTCCAAACTCTTCTGGACAACATTTTCCTTCCTCTGTTTGAGGTCACCATTG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 11
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagc-caattatatagtgttagcaattgatggtagttcttataaatgt---cttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
    |    | | |  |    ||  | |||    |  | |  |  | ||  |||  | ||    |||    ||  || ||  | || |  |  |    |||||| ||||||| || || ||||||||||| |||||||| || || ||||||||||| ||  | || ||||| |||||| |||| ||||||||||| ||| |  
----tcttaaccatgacaatgttacctttttccccagtgaaatatttagtgcaaaaacattacattattcttttctgatatattttgtggacattcttttgcagATTCCACGCTTATATAATGTGTACAAGGAAATGGGTATCGTTACATCATTCCAAAATCTTCTTGACAACATTTTCGTTCCTCTTTTTGAGGTTACTATTG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 11
--------------------------------aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaattat--atagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
                                  |      |    |   ||  |||  ||| |  || |   ||  | |    | |    |  | | ||    ||  | ||  |   | |   ||      |||| ||||| ||||||||  | ||||| || ||||| ||||||||||| |||||||| || || |||||||| |||||||| || ||||| | ||| ||  
gttagccatctctttgatacttgtgtgctccatgtccttccatgagtgtatgtgttttttttgtctccgtgtgtttgtaacatgactgctaactgagctatattttccttgttttctgtttgtctgctcactagCTCCCACGCTTGTACAACATTTACAAGGACATGGGTATTGTGACATCGTTCCAGAATATCCTGGACAATATATTCATTCCTCTGTTTGAAGCCACGGTAG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 11
aatttggggagcttttcctgcttttcatttattgccttaatttgctcagccaa----ttatatagtgttagcaat-tgatggtagttcttataaatgtcttgc-agCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
       |||   | ||   | |  ||||  | |  ||  || ||  |  |||    ||  ||  |||||    | | ||||||     |     ||| || | ||||||| ||| |||| ||||||||||| || ||||||||||| |||||||| ||||||||||| |||||||| ||  |||| || |||||||| ||||| |
-----ctggaatgtatctaacctgacattc-tggggtttgttagcaaaagcaaaatgttggattttgttattgttcttatggtataatatccttctgtttttccagCTTCCCCGGCTGTATAATGTGTACAAGGATATGGGAATTGTTACATCATTTCAGAACATGCTGGACAATATCTTTCTTCCCCTGTTTGAGGTTACTGTGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|7925052|gb|AW831078.1|AW831078
EST:     GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAG                         CTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
genomic: GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAGgtattcttta ... tgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
EST: gi|254332340|gb|GR846385.1|GR846385
EST:     GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAG                         CTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC
genomic: GGATAGTGAATAATGATTTGTACAGCGAGAATGTCGTTTGGTTGATTCAGgtattcttta ... tgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagccaattatatagtgttagcaattgatggtagttcttataaatgtcttgcagCTTCCACGGTTGTACAATGTGTACAAAGAAATGGGAATTGTGACATCATTCCAGAACATGCTCGACAATATTTTCATTCCACTTTTTGAGGTCACTGTCA
                       aattgat  putative branch site (score: 4)
      aattatatagtgtta  TA-rich tract